To give a perspective on the FE villain case, let's look at
CYL7. Ignoring Veronica and Edelgard (who won 2 and 4 respectively) the only villains present in the Top 20 characters overall is Black Knight, that's it. If you extend that to the Top 20 gender categories you add Lyon and Reinhardt, but the latter is more a product of his status in FEH then his villainy in Thracia. So, of forty characters, only three villains are present, and of the one that is extremely popular he's still outshined by Ike, Micaiah, and Soren as said before, with Elincia also being in contention.
Villains rarely stand out in FE, for as many complaints as they get, many of the lords tend to be the most popular of their games, if not the most popular. Even if Sakurai was reaching for the most popular characters in their respective games he'd still land at Ike, Marth, Roy, Lucina, Chrom and the like.